CheckCIF-CELLZ01
PROC-NAME: CELLZ01 Type_1
PURPOSE: To check that the cell contents calculated from _chemical_formula_sum and _cell_formula_units_Z matches that from the atom sites present in the _atom_site_ list and the _symmetry_ information.
PROCEDURE:
SUMMATION
(1) For each atomic species in the _chemical_formula_sum string, calculate the number of atoms in the cell using the _chemical_formula_sum counts and the _cell_formula_units_Z.
(2) For each atomic species in the _atom_site_ list, calculate, using the _atom_site_occupancy value and the symmetry site-multiplicity value (generated from NSYM), the number of atoms in the cell.
CALCULATE
DN = [cell contents from (1)]-[cell contents from (2)] for each atom type
SUMDN = sum of DN for ALL atom species
TEST
IF atom counts in (1) differ from those declared in the _atom_type_ list (if present) issue General ALERT
"WARNING: Cell contents from the formula and atom_type data differ!"
There is a discrepancy between the total number of each element in the unit cell calculated from Z * _chemical_formula_sum and that given in the loop structure:
loop_
_atom_type_symbol
_atom_type_description
_atom_type_number_in_cell
Check that the entries under _cell_formula_units_Z, _chemical_formula_sum and in the above loop are given correctly and completely. _chemical_formula_sum must correspond with the true sum of all elements in all distinct moieties present, including any solvent and all H atoms, and not the contents implied by the model if there are differences due to the omission of a few H atoms or solvent atoms.
If multiple moieties such as solvent are present, or one of the moieties possesses or is disordered about a crystallographic symmetry element, ensure that the correct ratio of moieties has been allowed for in the calculation of Z and _chemical_formula_sum.
_chemical_formula_sum must also be in the correct format (e.g. do not use subscript formatting: C10 H20 is correct, C~10~ H~20~ is not).
IF H-M space group mismatches Hall symbol issue General ALERT
"Input H-M symbol mismatch with Hall symbol"
Check that the entries given under _symmetry_space_group_name_H-M and _symmetry_space_group_name_Hall refer to the same space group and setting and do not have typographical errors. Note that space group symbols under _symmetry_space_group_name_H-M should not have typesetting formatting included (e.g. subscripts).
Example:
The following is the strictly correct way to represent space group 14.
_symmetry_space_group_name_H-M 'P 1 21/c 1'
Also interpreted correctly by CHECKCIF is:
_symmetry_space_group_name_H-M 'P 21/c'
Incorrect are:
_symmetry_space_group_name_H-M 'P 2(1)/c'
_symmetry_space_group_name_H-M 'P 2~1~/c'
IF SUMDN > 0.05 issue the General ALERT
"Difference between formula and atom_site contents detected."
AND THEN
IF SUMDN < 0.5 issue the General ALERT
"ALERT: Check formula stoichiometry or atom site occupancies."
There is a difference between the atom count derived from _chemical_formula_sum and from the _atom_site_ list (i.e the list of atomic coordinates). Check that _chemical_formula_sum is given correctly and in the correct format (e.g. do not use subscript formatting: C10 H20 is correct, C~10~ H~20~ is not).
Of course, _chemical_formula_sum must correspond with the true sum of all elements in all distinct moieties present, including any solvent and all H atoms, and not the contents implied by the model if there are differences due to the omission of a few H atoms or solvent atoms. In this case, this message can be ignored. However, be sure that the model is indeed otherwise complete and that no elements have been misassigned.
If multiple moieties such as solvent are present, or one of the moieties possesses or is disordered about a crystallographic symmetry element, ensure that the correct ratio of moieties has been allowed for in the calculation of Z and _chemical_formula_sum.
_chemical_formula_sum must also be in the correct format (e.g. do not use subscript formatting: C10 H20 is correct, C~10~ H~20~ is not).
Also check that the atom site occupancy is correct for the atomic coordinates otherwise a mismatch may be encountered [e.g an atom on a 2-fold axis normally has a site occupancy of 1.0 (but a multiplicity of 0.5)]. Furthermore, the site occupancy for disordered atomic sites should always sum to 1.0 when all of the alternative disordered sites are considered.
IF DN for Hydrogen atoms > 0.5 issue the General ALERT
"WARNING: H atoms missing from atom site list. Is this intentional?"
H atoms must be included in the model as far as possible. Exceptions might be where the H atoms cannot be located and their positions cannot otherwise be calculated or predicted from geometrical considerations. For example, with solvent or coordinated water H atoms or in severely disordered groups or solvent molecules.
ELSE issue the General ALERT
"ALERT: Large difference may be due to symmetry error - see SYMMG tests."
(http://journals.iucr.org/services/cif/checking/CELLZ_01.html)
目的：检查从“_chemical_formula_sum”和“_cell_formula_units_Z”计算得到的晶胞内容与存在于“_atom_site_”列表和“_symmetry_”信息的原子位置信息是否一致。
(1) 对于化学式总和(_chemical_formula_sum)字符串中的每个原子种类，用化学式总和(_chemical_formula_sum)计数和晶胞中分子个数(_cell_formula_units_Z)来计算原子数目。
(2) 对于原子位置(_atom_site_)列表中的原子种类，用原子位置占有率(_atom_site_occupancy)数值及对称位点多重性数值(由NSYM产生)来计算晶胞中的原子数目。
若(1)中的原子计数与原子类型(_atom_type_)列表(若存在)中声明的那些不同，发布一般警告
"WARNING: Cell contents from the formula and atom_type data differ!"
晶胞中由Z和化学式总和(_chemical_formula_sum)的乘积得出的每种元素的总数与循环结构中给出的数值存在差异：
loop_
_atom_type_symbol
_atom_type_description
_atom_type_number_in_cell
检查晶胞中分子个数(_cell_formula_units_Z)、化学式总和(_chemical_formula_sum)以及上述循环结构中的各个条目是否正确并完整地给出。化学式总和(_chemical_formula_sum)必须与存在的所有不同片段中所有元素的真实和相一致，包括任何溶剂以及所有H原子。如果由于省略少数H原子或溶剂原子而引起差异，则不对应于模型所暗示的内容。
若存在多个组分例如溶剂，或者其中一个组分具有无序或关于晶体学对称元素无序，则要确保在计算Z值和化学式总(_chemical_formula_sum)时各组分的比例为正确且允许的。
化学式总(_chemical_formula_sum)必须使用正确的格式(例如不要使用下标格式：C10 H20是正确的格式；而C~10~ H~20~是错误的格式)。
若H-M空间群与Hall符号不匹配，发布一般警告
"Input H-M symbol mismatch with Hall symbol"
检查Hermann–Mauguin空间群符号(_symmetry_space_group_name_H-M)项和Hall空间群符号(_symmetry_space_group_name_Hall)项给出的词条是否引用相同的空间群和设置，并且没有排版错误。注意Hermann–Mauguin空间群符号(_symmetry_space_group_name_H-M)项中的空间群符号不应包括排版格式(例如下标等)。
例：
以下是空间群14的严格正确的表示。
_symmetry_space_group_name_H-M 'P 1 21/c 1'
同样能够被CHECKCIF正确识别的是：
_symmetry_space_group_name_H-M 'P 21/c'
不正确的是：
_symmetry_space_group_name_H-M 'P 2(1)/c'
_symmetry_space_group_name_H-M 'P 2~1~/c'
若SUMDN大于0.05，发布一般警告
"Difference between formula and atom_site contents detected."
若SUMDN小于0.5，发布一般警告
"ALERT: Check formula stoichiometry or atom site occupancies."
从化学式总和(_chemical_formula_sum)与原子位置(_atom_site_)列表(即原子坐标列表)导出的原子计数存在差异。检查化学式总和(_chemical_formula_sum)是否正确给出，格式是否正确(例如不要使用下标格式：C10 H20为正确格式；C~10~ H~20~为错误格式)。
当然，化学式总和(_chemical_formula_sum)必须与存在的所有不同片段中所有元素的真实和相一致，包括任何溶剂以及所有H原子。如果由于省略少数H原子或溶剂原子而引起差异，则不对应于模型所暗示的内容。在这种情况下，可以忽略此消息。但是，务必确保模型确实是完全的并且没有元素指认错误。
若存在多个组分例如溶剂，或者其中一个组分具有无序或关于晶体学对称元素无序，则要确保在计算Z值和化学式总(_chemical_formula_sum)时各组分的比例为正确且允许的。
化学式总和(_chemical_formula_sum)必须使用正确的格式(例如不要使用下标格式：C10 H20是正确的格式；而C~10~ H~20~是错误的格式)。
同样要检查原子位置占有率是否正确对应于原子坐标，否则可能遇到不匹配[例如一个位于二重轴上的原子通常位置占有率为1.0(但多重数为0.5)]。此外，当考虑到所有可替代的无序位置时，无序原子的占有率总和为1.0。
若H原子的DN大于0.5，发布一般警告
"WARNING: H atoms missing from atom site list. Is this intentional?"
H原子必须尽可能地包含在模型中。除非H原子不能被定位，并且其位置不能从几何角度计算或预测。例如，溶剂或配位水上的H原子，或者严重无序的基团或溶剂分子上的H原子。
否则发布一般警告
"ALERT: Large difference may be due to symmetry error - see SYMMG tests."
例：CELLZ01_ALERT_1_G Difference between formula and atom_site contents detected.
CELLZ01_ALERT_1_G ALERT: Large difference may be due to a symmetry error - see SYMMG tests
From the CIF: _cell_formula_units_Z 6
From the CIF: _chemical_formula_sum C65 H65 B0.67 F2.67 Fe N Ni O P4
TEST: Compare cell contents of formula and atom_site data
atom Z*formula cif sites diff
C 390.00 390.00 0.00
H 390.00 390.00 0.00
B 4.02 6.00 -1.98
F 16.02 24.00 -7.98
Fe 6.00 6.00 0.00
N 6.00 6.00 0.00
Ni 6.00 6.00 0.00
O 6.00 6.00 0.00
P 24.00 24.00 0.00
S 18.00 18.00 0.00
警告原因：分子式和Z值没有给对。
解决策略：在ins里给对分子式和Z值重新精修生成CIF。若使用Olex2软件，则可填好Z'后精修重新生成CIF即可。
